Targeted proteomics: a go-to-method

In our pursuit to implement the most up-to-date technologies, FACTS has included the use of targeted proteomics by LC-MS/MS in our laboratory, as it offers significant benefits for food testing.

In this article we discuss the concept of target analytes in food testing, and briefly explore targeted proteomics by LC-MS/MS and its applications.

Target analytes

Food products are highly complex biological samples. Therefore, selecting appropriate target analytes and test methods for those target analytes requires careful consideration.

A target analyte is a substance with known properties that is expected or thought to be in a sample. Indicators of the target analyte may be detected and measured by a range of testing methods, giving information on the presence or absence and the quantity of the analyte in a sample.

Food consists of four major biomolecules: carbohydrates, lipids, proteins, and nucleic acids; all of which can be considered as possible target analytes.

Generally speaking, carbohydrates and lipids do not contain any unique information that can serve as a ‘fingerprint’ for their detection in food samples, or for confirmation of their origin (where they came from). Therefore, the use of carbohydrates and lipids as target analytes in food analysis is limited.

Proteins and nucleic acids, however, are very useful target analytes in food analysis. This is because they contain unique ‘fingerprinting’ information: proteins consist of unique chains of amino acids that fold into complex 3D structures; and nucleic acids such as DNA (deoxyribonucleic acid) are made up of unique sequences of nucleotides. This ‘uniqueness’ allows for their simultaneous detection and identification in food samples.

Proteins as target analytes

There are 20 different amino acids that are able to combine into long chains to form a protein. The sequence of amino acids in the chain dictates the folding of the protein, and thus determines each protein’s unique 3D structure and specific function. Furthermore, the sequence of the amino acids that make up a protein is unique to every organism.

A method may detect a protein by its 3D structure or by its unique amino acid sequence, among other properties. When proteins denature, they lose their 3D structure. Thus, food processing may render some proteins undetectable by structure-recognising methods.

Hydrolysis and digestion cause proteins to fragment into short amino acid chains (between two and 50 amino acids) known as ‘peptides’. However, peptides resulting from food processing are generally stable in food samples – they are unlikely to break down further into their constituent single amino acids – and can be detected by peptide-based methods.

Targeted proteomics

Targeted proteomics by LC-MS/MS is a technique that separates peptides with certain properties from a mixture of extracted and hydrolysed proteins from a food sample, and then detects a predetermined group of peptides using their mass-to-charge ratios. The detected peptides are of particular interest; they have been carefully selected as target analytes to answer a specific analytical question.

Targeted proteomics can be used for a variety of food analyses, including allergen detection, meat speciation, adulteration testing, vegan testing and more. Considering that allergens and animal products are protein-based, targeted proteomics is particularly useful in these cases, as it is the proteins that are of analytical interest (and not necessarily the DNA or other biomolecules).

How does targeted proteomics by LC-MS/MS compare to PCR and ELISA?

For a full comparison between these three methods, click here.

If you would like to know more about targeted proteomics by LC-MS/MS, or how the capabilities of this method can support your testing needs, please contact us.

Other articles and resources you may be interested in:
FACTS Targeted Proteomics by LC-MS/MS
Benefits of Targeted Proteomics (by LC-MS/MS) for allergen detection
Comparing test methods: PCR, ELISA & Targeted Proteomics by LC-MS/MS
Analytical advancements in Targeted Proteomics
Method selection for allergen detection
Improving LC-MS/MS allergen testing result quantification
FACTS Testing Catalogue